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## R

r2R() - Method in class org.metaqtl.Chromosome
r2R(int, int) - Method in class org.metaqtl.Chromosome
  Re-scale the chromosome assuming that the distances and recombination fractions are based on the frequency of recombinant genotypes R instead of the real recombination fraction r.
R2r() - Method in class org.metaqtl.Chromosome
R2r(int, int) - Method in class org.metaqtl.Chromosome
  Re-scale the chromosome assuming that the distances and recombination fractions are based on the frequency of recombinant genotypes R instead of the real recombination fraction r.
R2r(double, int, int) - Static method in class org.metaqtl.util.OffspringManager
  This routine returns the recombination rate r for a given value of the propertion of recombibant genotypes R according to the cross design.
r2R(double, int, int) - Static method in class org.metaqtl.util.OffspringManager
  This routine returns the recombination rate r for a given value of the propertion of recombibant genotypes R according to the cross design.
rate - Variable in class org.metaqtl.EMResult
  The quadratric rate of convergence of the algorithm.
read(Reader) - Static method in class org.metaqtl.factory.DubiousLocusFactory
  This routine reads the list of dubious markers from the given file location and returns if succeed an array of `IBioLocus` objects.
read(BufferedReader) - Static method in class org.metaqtl.factory.EMResultFactory
read(Reader) - Static method in class org.metaqtl.factory.MapDBFactory
  This method reads a file formated as follows : map property1 property2 property3 ...
read(Reader) - Static method in class org.metaqtl.factory.MetaDicoFactory
read(InputStream) - Static method in class org.metaqtl.factory.MetaQtlAnalysisFactory
read(Reader) - Static method in class org.metaqtl.factory.MetaQtlAnalysisFactory
read(Reader) - Static method in class org.metaqtl.factory.MetaQtlModelFactory
  This method reads a file formated as follows : Chromosome \t Trait \t Model
read(Reader) - Static method in class org.metaqtl.factory.TreeFactory
read(String) - Static method in class org.metaqtl.factory.TreeFactory
read_newick(Reader) - Static method in class org.metaqtl.factory.TreeFactory
read_newick(String) - Static method in class org.metaqtl.factory.TreeFactory
rebuildPartition(String[]) - Method in class org.metaqtl.QtlPartition
recombination(double, int, int) - Static method in class org.metaqtl.util.MappingFunction
  Returns the recombination rate from the distance.
removeAllele(String) - Method in class org.thalia.bio.entity.AlleleContainer
removeAllele(String) - Method in interface org.thalia.bio.IBioLocus
removeGroup(String) - Method in class org.thalia.bio.entity.GroupContainer
removeGroup(String) - Method in interface org.thalia.bio.IBioGenome
removeIndividual(String) - Method in class org.thalia.bio.entity.IndividualContainer
removeIndividual(String) - Method in interface org.thalia.bio.IBioPopulation
removeLocus(IBioGenome[], String) - Static method in class org.metaqtl.main.MetaMain
removeLocus(String) - Method in class org.thalia.bio.entity.LocusContainer
removeLocus(String) - Method in interface org.thalia.bio.IBioLGroup
ResourceBioEntityQuery - Class in org.thalia.bio.util
  This class makes it possible to make request on resource content using an array of requested entities.
ResourceBioEntityQuery() - Constructor for class org.thalia.bio.util.ResourceBioEntityQuery
resultByChrom - Variable in class org.metaqtl.MetaQtlAnalysis
  The matrix of results where the rows are the chromosomes.
RF - Static variable in interface org.thalia.bio.IBioCrossTypes
RIGHT_LABEL - Static variable in class org.metaqtl.graph.ChromLayer
RIGHT_LABEL - Static variable in class org.metaqtl.graph.ChromShape
RILSe - Static variable in interface org.thalia.bio.IBioCrossTypes
RILSi - Static variable in interface org.thalia.bio.IBioCrossTypes
root - Variable in class org.metaqtl.Tree
  The root of the tree.
root - Variable in class org.thalia.bio.entity.bean.OntologyBean
  The root of the ontology.
rsd - Variable in class org.metaqtl.MetaChrom
  The standardized residual between original marker intervals and those of the meta chromosome.
rsd - Variable in class org.metaqtl.MultiFitResult
  The residual standard deviations.
rsquare - Variable in class org.metaqtl.Qtl.QTLStats
  The r-square, i.e the proportion of variance explained by the QTL.
rtsafe(NumericalUtilities.NRFunction, double, double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
run(Chromosome, Chromosome) - Static method in class org.metaqtl.algo.CMSAlgorithm
  This methods find the common marker sequences between the two given chromosomes.
run(double[], double[]) - Static method in class org.metaqtl.algo.HClustAlgorithm
  This method performs a agglomerative clustering of the given data points where `x` is the vector of observed values and `sd` the vector of their standard deviations.
run() - Method in class org.metaqtl.algo.MetaMapAlgorithm
  This method builds a consensus genetic map from the given array of `maps`.
run() - Method in class org.metaqtl.algo.QtlClustAlgorithm
  This method performs a QTL meta-analysis on each chromosome of the given map.
run() - Method in class org.metaqtl.algo.QtlProjAlgorithm
  This routine performs the projection of the QTL from the maps onto the skeleton and returns the chromosomes on which the projection has been done.
run() - Method in class org.metaqtl.algo.QtlTreeAlgorithm
  This method performs an agglomerative hierarchical QTL clustering on each chromosome and returns the result as a `MetaQtlAnalysis` object.
run() - Method in interface org.metaqtl.IMetaAlgorithm
  Run the algorithm.

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